| OpenMS 2.5.0

MapAlignmentAlgorithmKD.h
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31 // $Maintainer: Johannes Veit $
32 // $Authors: Johannes Veit $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureMaps.h>
38 #include <OpenMS/ANALYSIS/MAPMATCHING/TransformationModelLowess.h>
39
40 namespace OpenMS
41 {
42
61 class OPENMS_DLLAPI MapAlignmentAlgorithmKD
62 {
63 public:
64
66 MapAlignmentAlgorithmKD(Size num_maps, const Param& param);
67
69 virtual ~MapAlignmentAlgorithmKD();
70
72 void addRTFitData(const KDTreeFeatureMaps& kd_data);
73
75 void fitLOWESS();
76
78 void transform(KDTreeFeatureMaps& kd_data) const;
79
80 protected:
81
82 virtual void updateMembers_();
83
85 Size computeCCs_(const KDTreeFeatureMaps& kd_data, std::vector<Size>& cc_index) const;
86
88 void getCCs_(const KDTreeFeatureMaps& kd_data, std::map<Size, std::vector<Size> >& result) const;
89
91 void filterCCs_(const KDTreeFeatureMaps& kd_data, const std::map<Size, std::vector<Size> >& ccs, std::map<Size, std::vector<Size> >& filtered_ccs) const;
92
93 private:
94
96 MapAlignmentAlgorithmKD();
97
99 std::vector<TransformationModel::DataPoints> fit_data_;
100
102 std::vector<TransformationModelLowess*> transformations_;
103
105 Param param_;
106
108 double max_pairwise_log_fc_;
109
111 double rt_tol_secs_;
112
114 double mz_tol_;
115
117 bool mz_ppm_;
118
119 };
120
121 } // namespace OpenMS
122
TransformationModelLowess.h
OpenMS::MapAlignmentAlgorithmKD::max_pairwise_log_fc_
double max_pairwise_log_fc_
Maximum absolute log10 fold change threshold between compatible features.
Definition: MapAlignmentAlgorithmKD.h:108
OpenMS::MapAlignmentAlgorithmKD::mz_tol_
double mz_tol_
m/z tolerance
Definition: MapAlignmentAlgorithmKD.h:114
OpenMS::KDTreeFeatureMaps
Stores a set of features, together with a 2D tree for fast search.
Definition: KDTreeFeatureMaps.h:49
OpenMS::MapAlignmentAlgorithmKD::rt_tol_secs_
double rt_tol_secs_
RT tolerance.
Definition: MapAlignmentAlgorithmKD.h:111
OpenMS::MapAlignmentAlgorithmKD::mz_ppm_
bool mz_ppm_
m/z unit ppm?
Definition: MapAlignmentAlgorithmKD.h:117
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MapAlignmentAlgorithmKD
An efficient reference-free feature map alignment algorithm for unlabeled data.
Definition: MapAlignmentAlgorithmKD.h:61
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::MapAlignmentAlgorithmKD::fit_data_
std::vector< TransformationModel::DataPoints > fit_data_
RT data for fitting the LOWESS.
Definition: MapAlignmentAlgorithmKD.h:99
OpenMS::MapAlignmentAlgorithmKD::transformations_
std::vector< TransformationModelLowess * > transformations_
LOWESS transformations.
Definition: MapAlignmentAlgorithmKD.h:102
OpenMS::MapAlignmentAlgorithmKD::param_
Param param_
Parameters.
Definition: MapAlignmentAlgorithmKD.h:105
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
KDTreeFeatureMaps.h