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ClusteredMS2ConsensusSpectrum.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 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
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16 // For a full list of authors, refer to the file AUTHORS.
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18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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29 //
30 // --------------------------------------------------------------------------
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>
57 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/MS2ConsensusSpectrum.h>
58
59 namespace OpenMS
60 {
61
62 class SUPERHIRN_DLLAPI ClusteredMS2ConsensusSpectrum :
63 public MS2ConsensusSpectrum
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
82 ~ClusteredMS2ConsensusSpectrum();
83
84 // class constructor
85 ClusteredMS2ConsensusSpectrum() {}
86 ClusteredMS2ConsensusSpectrum(MS2Fragment *);
87 ClusteredMS2ConsensusSpectrum(MS2ConsensusSpectrum *);
88 ClusteredMS2ConsensusSpectrum(double, double, int, int);
89
90 // class copy constructor
91 ClusteredMS2ConsensusSpectrum(const ClusteredMS2ConsensusSpectrum &);
92 // class copy constructor
93 ClusteredMS2ConsensusSpectrum(const ClusteredMS2ConsensusSpectrum *);
94
96 // overload operators:
97 //ClusteredMS2ConsensusSpectrum& operator=(const ClusteredMS2ConsensusSpectrum&);
98 bool operator==(const ClusteredMS2ConsensusSpectrum &);
99 ClusteredMS2ConsensusSpectrum & operator<=(const ClusteredMS2ConsensusSpectrum &);
100 ClusteredMS2ConsensusSpectrum & operator>=(const ClusteredMS2ConsensusSpectrum &);
101 ClusteredMS2ConsensusSpectrum & operator<(const ClusteredMS2ConsensusSpectrum &);
102 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
OpenMS::MS2Fragment
Definition: MS2Fragment.h:60
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::ClusteredMS2ConsensusSpectrum
Definition: ClusteredMS2ConsensusSpectrum.h:62
MS2ConsensusSpectrum.h
Types.h
OpenMS::ClusteredMS2ConsensusSpectrum::ClusteredMS2ConsensusSpectrum
ClusteredMS2ConsensusSpectrum()
Definition: ClusteredMS2ConsensusSpectrum.h:85
OpenMS::ClusteredMS2ConsensusSpectrum::MS2Scans
std::vector< int > MS2Scans
Definition: ClusteredMS2ConsensusSpectrum.h:75
OpenMS::MS2ConsensusSpectrum
Definition: MS2ConsensusSpectrum.h:64
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806