OpenMS
FeatureDeconvolution.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow $
6 // $Authors: $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 // OpenMS
17 
19 #include <map>
20 
21 namespace OpenMS
22 {
23 
24  class Compomer;
25 
34  class OPENMS_DLLAPI FeatureDeconvolution :
35  public DefaultParamHandler
36  {
37 public:
38 
39  enum CHARGEMODE {QFROMFEATURE = 1, QHEURISTIC, QALL};
40 
44 
50 
53 
56 
60 
71  void compute(const FeatureMap& fm_in, FeatureMap& fm_out, ConsensusMap& cons_map, ConsensusMap& cons_map_p);
72 
73 protected:
74 
75  void updateMembers_() override;
76 
82  struct CmpInfo_;
83 
84  /*
85  @brief test for obviously wrong parameter settings and warn
86 
87  Currently supports the following scenarios:
88  * 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)
89  When more than 5% of the cf's look like this, we report it.
90 
91  */
92  void checkSolution_(const ConsensusMap& cons_map) const;
93 
98  void inferMoreEdges_(PairsType& edges, std::map<Size, std::set<CmpInfo_> >& feature_adducts);
99 
101  void printEdgesOfConnectedFeatures_(Size idx_1, Size idx_2, const PairsType& feature_relation);
102 
109  inline bool intensityFilterPassed_(const Int q1, const Int q2, const Compomer& cmp, const Feature& f1, const Feature& f2) const;
110 
117  bool chargeTestworthy_(const Int feature_charge, const Int putative_charge, const bool other_unchanged) const;
118 
122  std::map<Size, String> map_label_;
124  std::map<String, Size> map_label_inverse_;
131 
132  };
133 } // namespace OpenMS
Holds information on an edge connecting two features from a (putative) charge ladder.
Definition: Compomer.h:33
A container for consensus elements.
Definition: ConsensusMap.h:66
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
An algorithm to decharge features (i.e. as found by FeatureFinder).
Definition: FeatureDeconvolution.h:36
bool intensityFilterPassed_(const Int q1, const Int q2, const Compomer &cmp, const Feature &f1, const Feature &f2) const
returns true if the intensity filter was passed or switched off
FeatureDeconvolution & operator=(const FeatureDeconvolution &source)
Assignment operator.
bool chargeTestworthy_(const Int feature_charge, const Int putative_charge, const bool other_unchanged) const
determines if we should test a putative feature charge
DPosition< 2 > ClusterPointType
Definition: FeatureDeconvolution.h:41
void compute(const FeatureMap &fm_in, FeatureMap &fm_out, ConsensusMap &cons_map, ConsensusMap &cons_map_p)
Compute a zero-charge feature map from a set of charged features.
bool enable_intensity_filter_
status of intensity filter for edges
Definition: FeatureDeconvolution.h:126
void checkSolution_(const ConsensusMap &cons_map) const
CHARGEMODE
Definition: FeatureDeconvolution.h:39
CHARGEMODE q_try_
status of charge discovery
Definition: FeatureDeconvolution.h:128
std::map< Size, String > map_label_
labeling table
Definition: FeatureDeconvolution.h:122
~FeatureDeconvolution() override
destructor
Feature::CoordinateType CoordinateType
Definition: FeatureDeconvolution.h:42
void inferMoreEdges_(PairsType &edges, std::map< Size, std::set< CmpInfo_ > > &feature_adducts)
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
MassExplainer::AdductsType potential_adducts_
List of adducts used to explain mass differences.
Definition: FeatureDeconvolution.h:120
std::map< String, Size > map_label_inverse_
labeling table inverse
Definition: FeatureDeconvolution.h:124
FeatureDeconvolution()
default constructor
Int verbose_level_
amount of debug information displayed
Definition: FeatureDeconvolution.h:130
FeatureDeconvolution(const FeatureDeconvolution &source)
Copy constructor.
void printEdgesOfConnectedFeatures_(Size idx_1, Size idx_2, const PairsType &feature_relation)
A function mostly for debugging.
ILPDCWrapper::PairsType PairsType
Definition: FeatureDeconvolution.h:43
A container for features.
Definition: FeatureMap.h:80
An LC-MS feature.
Definition: Feature.h:46
std::vector< ChargePair > PairsType
Definition: ILPDCWrapper.h:29
Adduct::AdductsType AdductsType
Definition: MassExplainer.h:33
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:38
int Int
Signed integer type.
Definition: Types.h:72
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19