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MS2Fragment.h
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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31 // $Maintainer: Florian Zeller $
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/CONCEPT/Types.h>
55 
56 namespace OpenMS
57 {
58 
59  class OPENMS_DLLAPI MS2Fragment
60  {
61 
62 
64  // declaration of the private members:
65 
66 private:
67 
69  // declaration of the public members:
70 
71  // AMRT tag
72  double precursorMZ;
74  double TR;
75  int scan;
76  int z;
77 
78  double fragmentMZ;
79  double intensityArea;
80 
81  // scan and TR ranges:
82  int scanStart;
83  int scanEnd;
84  double trStart;
85  double trEnd;
86 
87 
88 public:
89 
90  static int OutlierAttribute;
91 
92  // class destructor
93  ~MS2Fragment();
94 
95  // constructor for the object MS2Fragment:
96  MS2Fragment(double iPrecursorMZ, int iPrecursorCHRG, double iTR, int iScan, int iZ, double iFragmentMZ, double iIntensityArea,
97  int iScanStart, int iScanEnd, double iTrStart, double iTrEnd);
98  MS2Fragment(double iPrecursorMZ, int iPrecursorCHRG, double iTR, int iScan, int iZ, double iFragmentMZ, double iIntensityArea);
99 
100 
101  // class constructor
103  // class copy constructor
104  MS2Fragment(const MS2Fragment &);
105  // class copy constructor
106  MS2Fragment(const MS2Fragment *);
107 
108  // show info of the MS2 fragment
109  void show_info();
110 
111  // get the attribute of the fragment
112  // according to which outliers are removed
113  double getOutlierDetectionAttribute();
114 
115 
117  // overload operators:
118  MS2Fragment & operator=(const MS2Fragment &);
119  bool operator==(const MS2Fragment &);
120  MS2Fragment & operator<=(const MS2Fragment &);
121  MS2Fragment & operator>=(const MS2Fragment &);
122  MS2Fragment & operator<(const MS2Fragment &);
123  MS2Fragment & operator>(const MS2Fragment &);
124 
125 
127  // start here all the get / set
128  // function to access the
129  // variables of the class
130 
131 
132  // get hte averaged precurso mass:
133  double getPrecursorMZ(){ return precursorMZ; }
134  void setPrecursorMZ(double iMZ){ precursorMZ = iMZ; }
135  // get hte averaged precurso chrg:
136  int getPrecursorCHRG(){ return precursorCHRG; }
137  // retention time:
138  double getTR(){return TR; }
139  // start TR:
140  double getStartTR(){return trStart; }
141  // end TR:
142  double getEndTR(){return trEnd; }
143  // get the Fragment MZ:
144  double getFragmentMz(){return fragmentMZ; }
145  void setFragmentMz(double iMz){fragmentMZ = iMz; }
146  // get teh charge state:
147  int getCHRG(){return z; }
148  // get the apex scan:
149  int getApexScan(){return scan; }
150  // get the apex scan:
151  int getStartScan(){return scanStart; }
152  // get the apex scan:
153  int getEndScan(){return scanEnd; }
154 
155  // get the integrated peak area:
156  double getFragmentPeakArea(){return intensityArea; }
157  void setFragmentPeakArea(double iIntens){intensityArea = iIntens; }
158 
159 
160  };
161 
162 } // ns
163 
164 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MS2FRAGMENT_H
void setFragmentPeakArea(double iIntens)
Definition: MS2Fragment.h:157
double getFragmentMz()
Definition: MS2Fragment.h:144
int z
Definition: MS2Fragment.h:76
double getEndTR()
Definition: MS2Fragment.h:142
int getEndScan()
Definition: MS2Fragment.h:153
MS2Fragment()
Definition: MS2Fragment.h:102
double trEnd
Definition: MS2Fragment.h:85
double getFragmentPeakArea()
Definition: MS2Fragment.h:156
int getPrecursorCHRG()
Definition: MS2Fragment.h:136
int getApexScan()
Definition: MS2Fragment.h:149
static int OutlierAttribute
Definition: MS2Fragment.h:90
void setFragmentMz(double iMz)
Definition: MS2Fragment.h:145
double intensityArea
Definition: MS2Fragment.h:79
double precursorMZ
Definition: MS2Fragment.h:72
int scan
Definition: MS2Fragment.h:75
double fragmentMZ
Definition: MS2Fragment.h:78
int getStartScan()
Definition: MS2Fragment.h:151
int scanEnd
Definition: MS2Fragment.h:83
double getTR()
Definition: MS2Fragment.h:138
int scanStart
Definition: MS2Fragment.h:82
int precursorCHRG
Definition: MS2Fragment.h:73
double getStartTR()
Definition: MS2Fragment.h:140
double getPrecursorMZ()
Definition: MS2Fragment.h:133
int getCHRG()
Definition: MS2Fragment.h:147
double TR
Definition: MS2Fragment.h:74
Definition: MS2Fragment.h:59
double trStart
Definition: MS2Fragment.h:84
void setPrecursorMZ(double iMZ)
Definition: MS2Fragment.h:134

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:17 using doxygen 1.8.5