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MSPeak.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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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 #pragma once
50
51 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
52
53 #include <string>
54 #include <vector>
55 #include <map>
56
57 #include <OpenMS/CONCEPT/Types.h>
58 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/CentroidPeak.h>
59
60 namespace OpenMS
61 {
62
63 //class CentroidPeak; // changed to include
64
65 class SUPERHIRN_DLLAPI MSPeak
66 {
67
69 // declaration of the private members:
70
71 double precursorMZ;
72 double MZ;
73 float INTENSITY;
74 int SCAN;
75 double TR;
76 unsigned int CHRG;
77 unsigned int NRISOTOPES;
78 float SCORE;
79
80 std::string extraMSPeakInfo;
81
82 // child scan options:
83 bool precursorMass;
84 int childScan;
85
86 double SignalToNoise;
87 std::vector<CentroidPeak> ISOPEAKS;
88
89 private:
90
92 // declaration of the public members:
93
94 public:
95
96 // class destructor
97 ~MSPeak();
98
99 // class constructor
100 MSPeak(int, double, float);
101 MSPeak();
102 MSPeak(int, double, float, unsigned int, unsigned int, float, std::vector<CentroidPeak>);
103 MSPeak(const MSPeak &);
104 MSPeak(const MSPeak *);
105
107 // overload operators:
108 MSPeak & operator=(const MSPeak &);
109 MSPeak & operator<=(const MSPeak &);
110 MSPeak & operator>=(const MSPeak &);
111 MSPeak & operator<(const MSPeak &);
112 MSPeak & operator>(const MSPeak &);
113
114 // show content of peak:
115 void show_info();
116
117 // store the MS/MS scan number and activate this peak as precursor peak:
118 void activateAsPrecursorPeak(int);
119
121 // check if the input mass matches one of the isotopic masses
122 bool checkIsotopeBelongingAndAdjustMass(double, double);
123
125 // start here all the get / set
126 // function to access the
127 // variables of the class
128
129 std::vector<CentroidPeak> & get_isotopic_peaks();
130
131 std::vector<CentroidPeak>::iterator get_isotopic_peaks_start();
132
133 std::vector<CentroidPeak>::iterator get_isotopic_peaks_end();
134
135 void setExtraPeakInfo(std::string in);
136
137 std::string getExtraPeakInfo();
138
139 // precursor mass of the MS2 scan:
140 void setPrecursorMZ(double in);
141
142 double getPrecursorMZ();
143
144 // precursor mass charge state:
145 void setPrecursorCHRG(int in);
146
147 int getPrecursorCHRG();
148
149 // check if this peak has been determined as precursor:
150 bool getPrecursorActivation();
151
152 int get_Chrg();
153
154 void set_Chrg(int z);
155
156 int get_Scan();
157
158 float get_intensity();
159
160 double get_MZ();
161
162 int get_scan_number();
163
164 void set_retention_time(double in);
165
166 double get_retention_time();
167
168 unsigned int get_charge_state();
169
170 unsigned int get_nr_isotopes();
171
172 float get_score();
173
174 double getSignalToNoise();
175
176 void setSignalToNoise(double in);
177
178 };
179
180 } // ns
181
OpenMS::MSPeak::precursorMass
bool precursorMass
Definition: MSPeak.h:83
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::MSPeak::precursorMZ
double precursorMZ
Definition: MSPeak.h:71
OpenMS::MSPeak::childScan
int childScan
Definition: MSPeak.h:84
Types.h
OpenMS::MSPeak
Definition: MSPeak.h:65
OpenMS::MSPeak::SCAN
int SCAN
Definition: MSPeak.h:74
OpenMS::MSPeak::SCORE
float SCORE
Definition: MSPeak.h:78
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MSPeak::SignalToNoise
double SignalToNoise
Definition: MSPeak.h:86
CentroidPeak.h
OpenMS::MSPeak::NRISOTOPES
unsigned int NRISOTOPES
Definition: MSPeak.h:77
OpenMS::MSPeak::MZ
double MZ
Definition: MSPeak.h:72
OpenMS::MSPeak::INTENSITY
float INTENSITY
Definition: MSPeak.h:73
OpenMS::MSPeak::ISOPEAKS
std::vector< CentroidPeak > ISOPEAKS
Definition: MSPeak.h:87
OpenMS::MSPeak::TR
double TR
Definition: MSPeak.h:75
OpenMS::MSPeak::extraMSPeakInfo
std::string extraMSPeakInfo
Definition: MSPeak.h:80
OpenMS::MSPeak::CHRG
unsigned int CHRG
Definition: MSPeak.h:76