Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
LCMSCData.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
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
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMSCDATA_H
51 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMSCDATA_H
52 
53 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
54 
56 
57 namespace OpenMS
58 {
59 
60  class SUPERHIRN_DLLAPI LCMSCData
61  {
62 public:
63  typedef std::map<int, LCElutionPeak> elution_peak_list;
64  typedef std::map<int, LCElutionPeak>::iterator elution_peak_list_ITERATOR;
65  typedef std::map<double, elution_peak_list> MZ_LIST;
66  typedef MZ_LIST::iterator MZ_LIST_ITERATOR;
67 
68  LCMSCData();
69  LCMSCData(const LCMSCData &);
70  LCMSCData(const LCMSCData *);
71  virtual ~LCMSCData();
72 
74  // overload operators:
75  LCMSCData & operator=(const LCMSCData &);
76 
78  // start here all the get / set
79  // function to access the
80  // variables of the class
81 
82  // start / end of the mz list:
83  MZ_LIST_ITERATOR get_DATA_start();
84  MZ_LIST_ITERATOR get_DATA_end();
85 
86  // find data of a specific m/z:
87  MZ_LIST_ITERATOR get_MZ_by_iterator(double);
88  // add data into the structure:
89  void add_LC_elution_peak(double, LCElutionPeak *);
90 
91  // get a list of m/z observed in a scan +/- scan_tolerance:
92  // return the area of the LC elution peaks
93  std::vector<LCElutionPeak> get_MZ_list(int);
94  std::vector<LCElutionPeak> get_MZ_list(int, int);
95 
96  // get all extracted LC peaks:
97  std::vector<LCElutionPeak *> get_ALL_peak();
98  // get a vector with all LC peaks ordered by their score:
99  std::vector<LCElutionPeak *> get_ALL_peak_ordered();
100 
101 
102  /*
104  // operator which compares LC elution peaks
105  // by their score:
106  struct OPERATOR_LC_PEAK{
107  bool operator()(LCElutionPeak* A,LCElutionPeak* B) const{
108  return A->get_LC_score() < B->get_LC_score();
109  }
110  };
111  */
112 
113  // minimal MS peak intensity allowed:
114  // static float intensity_min_threshold;
115 
116 
117 
118 protected:
119 
120  // main data structure:
121  MZ_LIST DATA;
122 
123 
124  };
125 
126 } // ns
127 
128 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMSCDATA_H
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::map< double, elution_peak_list > MZ_LIST
Definition: LCMSCData.h:65
MZ_LIST DATA
Definition: LCMSCData.h:121
Definition: LCElutionPeak.h:68
std::map< int, LCElutionPeak >::iterator elution_peak_list_ITERATOR
Definition: LCMSCData.h:64
std::map< int, LCElutionPeak > elution_peak_list
Definition: LCMSCData.h:63
MZ_LIST::iterator MZ_LIST_ITERATOR
Definition: LCMSCData.h:66
Definition: LCMSCData.h:60

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:01 using doxygen 1.8.13