| OpenMS 2.5.0

MS2Fragment.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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16 // For a full list of authors, refer to the file AUTHORS.
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20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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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
51 #pragma once
52
53 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
54
55 #include <OpenMS/CONCEPT/Types.h>
56
57 namespace OpenMS
58 {
59
60 class SUPERHIRN_DLLAPI MS2Fragment
61 {
62
63
65 // declaration of the private members:
66
67 private:
68
70 // declaration of the public members:
71
72 // AMRT tag
73 double precursorMZ;
74 int precursorCHRG;
75 double TR;
76 int scan;
77 int z;
78
79 double fragmentMZ;
80 double intensityArea;
81
82 // scan and TR ranges:
83 int scanStart;
84 int scanEnd;
85 double trStart;
86 double trEnd;
87
88
89 public:
90
91 static int OutlierAttribute;
92
93 // class destructor
94 ~MS2Fragment();
95
96 // constructor for the object MS2Fragment:
97 MS2Fragment(double iPrecursorMZ, int iPrecursorCHRG, double iTR, int iScan, int iZ, double iFragmentMZ, double iIntensityArea,
98 int iScanStart, int iScanEnd, double iTrStart, double iTrEnd);
99 MS2Fragment(double iPrecursorMZ, int iPrecursorCHRG, double iTR, int iScan, int iZ, double iFragmentMZ, double iIntensityArea);
100
101
102 // class constructor
103 MS2Fragment();
104 // class copy constructor
105 MS2Fragment(const MS2Fragment &);
106 // class copy constructor
107 MS2Fragment(const MS2Fragment *);
108
109 // show info of the MS2 fragment
110 void show_info();
111
112 // get the attribute of the fragment
113 // according to which outliers are removed
114 double getOutlierDetectionAttribute();
115
116
118 // overload operators:
119 MS2Fragment & operator=(const MS2Fragment &);
120 bool operator==(const MS2Fragment &);
121 MS2Fragment & operator<=(const MS2Fragment &);
122 MS2Fragment & operator>=(const MS2Fragment &);
123 MS2Fragment & operator<(const MS2Fragment &);
124 MS2Fragment & operator>(const MS2Fragment &);
125
126
128 // start here all the get / set
129 // function to access the
130 // variables of the class
131
132
133 // get the averaged precursor mass:
134 double getPrecursorMZ();
135 void setPrecursorMZ(double iMZ);
136 // get the averaged precursor charge:
137 int getPrecursorCHRG();
138 // retention time:
139 double getTR();
140 // start TR:
141 double getStartTR();
142 // end TR:
143 double getEndTR();
144 // get the Fragment MZ:
145 double getFragmentMz();
146 void setFragmentMz(double iMz);
147 // get the charge state:
148 int getCHRG();
149 // get the apex scan:
150 int getApexScan();
151 // get the apex scan:
152 int getStartScan();
153 // get the apex scan:
154 int getEndScan();
155
156 // get the integrated peak area:
157 double getFragmentPeakArea();
158 void setFragmentPeakArea(double iIntens);
159
160 };
161
162 } // ns
163
OpenMS::MS2Fragment::OutlierAttribute
static int OutlierAttribute
Definition: MS2Fragment.h:91
OpenMS::MS2Fragment::trStart
double trStart
Definition: MS2Fragment.h:85
OpenMS::MS2Fragment
Definition: MS2Fragment.h:60
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::MS2Fragment::precursorCHRG
int precursorCHRG
Definition: MS2Fragment.h:74
Types.h
OpenMS::MS2Fragment::trEnd
double trEnd
Definition: MS2Fragment.h:86
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MS2Fragment::scanEnd
int scanEnd
Definition: MS2Fragment.h:84
OpenMS::MS2Fragment::TR
double TR
Definition: MS2Fragment.h:75
OpenMS::MS2Fragment::scanStart
int scanStart
Definition: MS2Fragment.h:83
OpenMS::MS2Fragment::scan
int scan
Definition: MS2Fragment.h:76
OpenMS::MS2Fragment::z
int z
Definition: MS2Fragment.h:77
OpenMS::MS2Fragment::fragmentMZ
double fragmentMZ
Definition: MS2Fragment.h:79
OpenMS::MS2Fragment::precursorMZ
double precursorMZ
Definition: MS2Fragment.h:73
OpenMS::MS2Fragment::intensityArea
double intensityArea
Definition: MS2Fragment.h:80
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806