| OpenMS 2.5.0

MS1FeatureMerger.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Lukas Mueller, Markus Mueller $
33 // --------------------------------------------------------------------------
34 //
36 //
37 // written by Lukas N Mueller, 30.3.05
38 // Lukas.Mueller@imsb.biol.ethz.ch
39 // Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich
40 //
41 // Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
42 // December 2010
43 //
44 // **********************************************************************//
45 // CLASS Spec MERGER:
46 // merges 2 spectra which have been preprocessed
47 // by spec_merge-> common lc_peaks are marked!!!!
48 //
49
50 #pragma once
51
52 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
53
54 #include <vector>
55 #include <map>
56
57 namespace OpenMS
58 {
59 class LCMS;
60 class SHFeature;
61
62 class SUPERHIRN_DLLAPI MS1FeatureMerger
63 {
64
65
67 // declaration of the private members:
68
69 private:
70
72 // the common lc-ms spectrum,
73 // created from the overlap of A and B
74 LCMS * lcmsMap;
75
76 std::vector<int> idsToRemove;
77 std::map<double, std::vector<SHFeature *> > mzClusters;
78
79
81 // declaration of the public members:
82
83 public:
84
85 /*
86 static double INTENSITY_APEX_THRESHOLD;
87 static double MS1_PEAK_AREA_TR_RESOLUTION;
88
89 static double INITIAL_TR_TOLERANCE;
90 static double MS1_FEATURE_MERGING_TR_TOLERANCE;
91 static double PERCENTAGE_INTENSITY_ELUTION_BORDER_VARIATION;
92 static double PPM_TOLERANCE_FOR_MZ_CLUSTERING;
93 static bool MS1_FEATURE_CLUSTERING;
94 */
95
96 // class destructor
97 ~MS1FeatureMerger();
98 // class constructor
99 MS1FeatureMerger(LCMS *);
100
101
103 // start the merging process
104 void startFeatureMerging();
105 // create a distribution of delta Tr for the split features
106 void createMZFeatureClusters();
107 // process a vector of m/z features
108 void processMZFeatureVector(std::vector<SHFeature *> *);
109 // find to this feature the features which should be merged
110 std::vector<SHFeature *>::iterator findFeaturesToMerge(SHFeature *, std::vector<SHFeature *>::iterator, std::vector<SHFeature *> *);
111 // compare if a feature belongs to another feature
112 bool compareMZFeatureBeloning(SHFeature *, SHFeature *);
113 // merge the target to the search feature
114 void mergeFeatures(SHFeature *, SHFeature *);
115 // compute new parameters for the merged MS1 feature
116 void computeNewMS1FeatureParameters(SHFeature *);
117 // computes the area of between 2 peaks:
118 double computeDeltaArea(double, double, double, double);
119
120
121 // this structure provides the function to compare
122 // in the sorting algorithm:
123 struct OPERATOR_FEATURE_TR
124 {
125 // provide the compare function for sort:
126 bool operator()(const SHFeature A, const SHFeature B) const;
127 };
128 };
129
130 } // ns
131
OpenMS::MS1FeatureMerger::idsToRemove
std::vector< int > idsToRemove
Definition: MS1FeatureMerger.h:76
OpenMS::LCMS
Definition: LCMS.h:57
OpenMS::SHFeature
Definition: SHFeature.h:59
OpenMS::MS1FeatureMerger::OPERATOR_FEATURE_TR
Definition: MS1FeatureMerger.h:123
OpenMS::MS1FeatureMerger::mzClusters
std::map< double, std::vector< SHFeature * > > mzClusters
Definition: MS1FeatureMerger.h:77
OpenMS::MS1FeatureMerger
Definition: MS1FeatureMerger.h:62
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MS1FeatureMerger::lcmsMap
LCMS * lcmsMap
Definition: MS1FeatureMerger.h:74