OpenMS  2.5.0
ClusteredMS2ConsensusSpectrum.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Lukas Mueller, Markus Mueller $
33 // --------------------------------------------------------------------------
34 //
36 //
37 // PEAK DETECTION OF FOURIER TRANSFORME MS INSTRUMENT DATA
38 //
39 // written by Markus Mueller, markus.mueller@imsb.biol.ethz.ch
40 // ( and Lukas Mueller, Lukas.Mueller@imsb.biol.ethz.ch)
41 // October 2005
42 //
43 // Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
44 // December 2010
45 //
46 // Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich
47 //
48 //
49 
50 #pragma once
51 
52 
53 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
54 
55 #include <vector>
56 #include <OpenMS/CONCEPT/Types.h>
58 
59 namespace OpenMS
60 {
61 
62  class SUPERHIRN_DLLAPI ClusteredMS2ConsensusSpectrum :
64  {
65 
67  // declaration of the private members:
68 
69 private:
70 
72  // declaration of the public members:
73 
74  // stores the individual MS/MS spectra:
75  std::vector<int> MS2Scans;
76 
77 public:
78 
79  using MS2ConsensusSpectrum::operator=;
80 
81  // class destructor
83 
84  // class constructor
88  ClusteredMS2ConsensusSpectrum(double, double, int, int);
89 
90  // class copy constructor
92  // class copy constructor
94 
96  // overload operators:
97  //ClusteredMS2ConsensusSpectrum& operator=(const ClusteredMS2ConsensusSpectrum&);
103 
105  // trace the fragments across MS/MS scans runs:
106  void constructClusteredConsenusSpectraFragments(MS2ConsensusSpectrum *);
107 
108  // add a MS2 Consensus Spectrum:
109  void addMS2ConsensusSpectrum(MS2ConsensusSpectrum *);
110 
112  // extracts fragments from a MS/MS spectra and inserts
113  // them into the Clustered MS/MS spectrum:
114  void extractFragmentsFromSpectra(MS2ConsensusSpectrum *);
115  // merge a MS2 fragment into the target MS2 fragment:
116  void mergeMS2Fragments(MS2Fragment *, MS2Fragment *);
117 
118  // plot all the consensus MS2 spectrum in one plot:
119  void plotCombinedSpectra();
120 
121  // remove outlier fragments based on their:
122  // MS2Fragment::OutlierAttribute = ...
123  // 1: retention time
124  // 2: precursor mass
125  // etc.
126  void removeOutlierFragments();
127 
129  // start here all the get / set
130  // function to access the
131  // variables of the class
132 
133  int getNumberOfSpectraScan();
134 
135  std::vector<int>::iterator getSpectraScanNumberStart();
136 
137  std::vector<int>::iterator getSpectraScanNumberEnd();
138 
139  };
140 
141 } // ns
142 
Types.h
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MS2ConsensusSpectrum
Definition: MS2ConsensusSpectrum.h:64
MS2ConsensusSpectrum.h
OpenMS::MS2Fragment
Definition: MS2Fragment.h:60
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
OpenMS::ClusteredMS2ConsensusSpectrum::ClusteredMS2ConsensusSpectrum
ClusteredMS2ConsensusSpectrum()
Definition: ClusteredMS2ConsensusSpectrum.h:85
OpenMS::ClusteredMS2ConsensusSpectrum::MS2Scans
std::vector< int > MS2Scans
Definition: ClusteredMS2ConsensusSpectrum.h:75
OpenMS::ClusteredMS2ConsensusSpectrum
Definition: ClusteredMS2ConsensusSpectrum.h:62