Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
ClusteredMS2ConsensusSpectrum.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 2002-2013.
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: 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 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_CLUSTEREDMS2CONSENSUSSPECTRUM_H
51 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_CLUSTEREDMS2CONSENSUSSPECTRUM_H
52 
53 #include <vector>
54 #include <OpenMS/CONCEPT/Types.h>
56 
57 namespace OpenMS
58 {
59 
60  class OPENMS_DLLAPI ClusteredMS2ConsensusSpectrum :
62  {
63 
65  // declaration of the private members:
66 
67 private:
68 
70  // declaration of the public members:
71 
72  // stores the individual MS/MS spectra:
73  std::vector<int> MS2Scans;
74 
75 public:
76 
77  using MS2ConsensusSpectrum::operator=;
78 
79  // class destructor
81 
82  // class constructor
86  ClusteredMS2ConsensusSpectrum(double, double, int, int);
87 
88  // class copy constructor
90  // class copy constructor
92 
94  // overload operators:
95  //ClusteredMS2ConsensusSpectrum& operator=(const ClusteredMS2ConsensusSpectrum&);
96  bool operator==(const ClusteredMS2ConsensusSpectrum &);
101 
103  // trace the fragments across MS/MS scans runs:
104  void constructClusteredConsenusSpectraFragments(MS2ConsensusSpectrum *);
105 
106  // add a MS2 Consensus Spectrum:
107  void addMS2ConsensusSpectrum(MS2ConsensusSpectrum *);
108 
110  // extracts fragments from a MS/MS spectra and inserts
111  // them into the Clustered MS/MS spectrum:
112  void extractFragmentsFromSpectra(MS2ConsensusSpectrum *);
113  // merge a MS2 fragment into the target MS2 fragment:
114  void mergeMS2Fragments(MS2Fragment *, MS2Fragment *);
115 
116  // plot all the consensus MS2 spectrum in one plot:
117  void plotCombinedSpectra();
118 
119  // remove outlier fragments based on their:
120  // MS2Fragment::OutlierAttribute = ...
121  // 1: retention time
122  // 2: precursor mass
123  // etc.
124  void removeOutlierFragments();
125 
127  // start here all the get / set
128  // function to access the
129  // variables of the class
130 
132  {
133  return (int) MS2Scans.size();
134  }
135 
136  std::vector<int>::iterator getSpectraScanNumberStart()
137  {
138  return MS2Scans.begin();
139  }
140 
141  std::vector<int>::iterator getSpectraScanNumberEnd()
142  {
143  return MS2Scans.end();
144  }
145 
146  };
147 
148 } // ns
149 
150 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_CLUSTEREDMS2CONSENSUSSPECTRUM_H
std::vector< int >::iterator getSpectraScanNumberEnd()
Definition: ClusteredMS2ConsensusSpectrum.h:141
std::vector< int >::iterator getSpectraScanNumberStart()
Definition: ClusteredMS2ConsensusSpectrum.h:136
int getNumberOfSpectraScan()
Definition: ClusteredMS2ConsensusSpectrum.h:131
ClusteredMS2ConsensusSpectrum()
Definition: ClusteredMS2ConsensusSpectrum.h:83
std::vector< int > MS2Scans
Definition: ClusteredMS2ConsensusSpectrum.h:73
Definition: ClusteredMS2ConsensusSpectrum.h:60
Definition: MS2ConsensusSpectrum.h:62
Definition: MS2Fragment.h:59

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:12 using doxygen 1.8.5