Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
LabeledPairFinder.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: Marc Sturm $
33 // --------------------------------------------------------------------------
34 
35 #ifndef OPENMS_ANALYSIS_MAPMATCHING_LABELEDPAIRFINDER_H
36 #define OPENMS_ANALYSIS_MAPMATCHING_LABELEDPAIRFINDER_H
37 
39 
40 #include <boost/math/tr1.hpp>
41 #include <cmath>
42 
43 namespace OpenMS
44 {
57  class OPENMS_DLLAPI LabeledPairFinder :
58  public BaseGroupFinder
59  {
60 
61 public:
62 
65 
67  inline virtual ~LabeledPairFinder()
68  {
69  }
70 
73  {
74  return new LabeledPairFinder();
75  }
76 
78  static const String getProductName()
79  {
80  return "labeled_pair_finder";
81  }
82 
93  virtual void run(const std::vector<ConsensusMap> & input_maps, ConsensusMap & result_map);
94 
95 protected:
96 
98  inline double PValue_(double x, double m, double sig1, double sig2)
99  {
100  if (m < x)
101  {
102  return 1 - boost::math::tr1::erf((x - m) / sig2 / 0.707106781);
103  }
104  else
105  {
106  return 1 - boost::math::tr1::erf((m - x) / sig1 / 0.707106781);
107  }
108  }
109 
110 private:
111 
113  LabeledPairFinder(const LabeledPairFinder & source);
114 
116  LabeledPairFinder & operator=(const LabeledPairFinder & source);
117 
118  }; // end of class LabeledPairFinder
119 
120 } // end of namespace OpenMS
121 
122 #endif // OPENMS_ANALYSIS_MAPMATCHER_LABELEDPAIRFINDER_H
A more convenient string class.
Definition: String.h:57
static const String getProductName()
Returns the name of this module.
Definition: LabeledPairFinder.h:78
A container for consensus elements.
Definition: ConsensusMap.h:72
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
virtual ~LabeledPairFinder()
Destructor.
Definition: LabeledPairFinder.h:67
static BaseGroupFinder * create()
Returns an instance of this class.
Definition: LabeledPairFinder.h:72
The base class of all element group finding algorithms.
Definition: BaseGroupFinder.h:62
double PValue_(double x, double m, double sig1, double sig2)
return the p-value at position x for the bi-Gaussian distribution with mean m and standard deviation ...
Definition: LabeledPairFinder.h:98
The LabeledPairFinder allows the matching of labeled features (features with a fixed distance)...
Definition: LabeledPairFinder.h:57

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