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MS2Fragment.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 
51 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MS2FRAGMENT_H
52 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MS2FRAGMENT_H
53 
54 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
55 
56 #include <OpenMS/CONCEPT/Types.h>
57 
58 namespace OpenMS
59 {
60 
61  class SUPERHIRN_DLLAPI MS2Fragment
62  {
63 
64 
66  // declaration of the private members:
67 
68 private:
69 
71  // declaration of the public members:
72 
73  // AMRT tag
74  double precursorMZ;
76  double TR;
77  int scan;
78  int z;
79 
80  double fragmentMZ;
81  double intensityArea;
82 
83  // scan and TR ranges:
84  int scanStart;
85  int scanEnd;
86  double trStart;
87  double trEnd;
88 
89 
90 public:
91 
92  static int OutlierAttribute;
93 
94  // class destructor
95  ~MS2Fragment();
96 
97  // constructor for the object MS2Fragment:
98  MS2Fragment(double iPrecursorMZ, int iPrecursorCHRG, double iTR, int iScan, int iZ, double iFragmentMZ, double iIntensityArea,
99  int iScanStart, int iScanEnd, double iTrStart, double iTrEnd);
100  MS2Fragment(double iPrecursorMZ, int iPrecursorCHRG, double iTR, int iScan, int iZ, double iFragmentMZ, double iIntensityArea);
101 
102 
103  // class constructor
104  MS2Fragment();
105  // class copy constructor
106  MS2Fragment(const MS2Fragment &);
107  // class copy constructor
108  MS2Fragment(const MS2Fragment *);
109 
110  // show info of the MS2 fragment
111  void show_info();
112 
113  // get the attribute of the fragment
114  // according to which outliers are removed
115  double getOutlierDetectionAttribute();
116 
117 
119  // overload operators:
120  MS2Fragment & operator=(const MS2Fragment &);
121  bool operator==(const MS2Fragment &);
122  MS2Fragment & operator<=(const MS2Fragment &);
123  MS2Fragment & operator>=(const MS2Fragment &);
124  MS2Fragment & operator<(const MS2Fragment &);
125  MS2Fragment & operator>(const MS2Fragment &);
126 
127 
129  // start here all the get / set
130  // function to access the
131  // variables of the class
132 
133 
134  // get the averaged precursor mass:
135  double getPrecursorMZ();
136  void setPrecursorMZ(double iMZ);
137  // get the averaged precursor charge:
138  int getPrecursorCHRG();
139  // retention time:
140  double getTR();
141  // start TR:
142  double getStartTR();
143  // end TR:
144  double getEndTR();
145  // get the Fragment MZ:
146  double getFragmentMz();
147  void setFragmentMz(double iMz);
148  // get the charge state:
149  int getCHRG();
150  // get the apex scan:
151  int getApexScan();
152  // get the apex scan:
153  int getStartScan();
154  // get the apex scan:
155  int getEndScan();
156 
157  // get the integrated peak area:
158  double getFragmentPeakArea();
159  void setFragmentPeakArea(double iIntens);
160 
161  };
162 
163 } // ns
164 
165 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MS2FRAGMENT_H
int z
Definition: MS2Fragment.h:78
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
double trEnd
Definition: MS2Fragment.h:87
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
static int OutlierAttribute
Definition: MS2Fragment.h:92
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
double intensityArea
Definition: MS2Fragment.h:81
double precursorMZ
Definition: MS2Fragment.h:74
int scan
Definition: MS2Fragment.h:77
double fragmentMZ
Definition: MS2Fragment.h:80
int scanEnd
Definition: MS2Fragment.h:85
int scanStart
Definition: MS2Fragment.h:84
int precursorCHRG
Definition: MS2Fragment.h:75
double TR
Definition: MS2Fragment.h:76
Definition: MS2Fragment.h:61
double trStart
Definition: MS2Fragment.h:86

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13