Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
ThresholdMower.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 2002-2015.
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: Mathias Walzer $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 #ifndef OPENMS_FILTERING_TRANSFORMERS_THRESHOLDMOWER_H
36 #define OPENMS_FILTERING_TRANSFORMERS_THRESHOLDMOWER_H
37 
40 
41 namespace OpenMS
42 {
50  class OPENMS_DLLAPI ThresholdMower :
51  public DefaultParamHandler
52  {
53 public:
54 
55  // @name Constructors and Destructors
56  // @{
60  virtual ~ThresholdMower();
61 
63  ThresholdMower(const ThresholdMower & source);
65  ThresholdMower & operator=(const ThresholdMower & source);
66  // @}
67 
68  // @name Accessors
69  // @{
71 
73  template <typename SpectrumType>
74  void filterSpectrum(SpectrumType & spectrum)
75  {
76  // sort by intensity
77  spectrum.sortByIntensity();
78 
79  // find right position to erase
80  typename SpectrumType::PeakType p;
81  threshold_ = ((double)param_.getValue("threshold"));
82  p.setIntensity(threshold_);
83  spectrum.erase(
84  spectrum.begin(),
85  lower_bound(spectrum.begin(), spectrum.end(), p, typename SpectrumType::PeakType::IntensityLess())
86  );
87  }
88 
89  void filterPeakSpectrum(PeakSpectrum & spectrum);
90 
91  void filterPeakMap(PeakMap & exp);
92 
93  //TODO reimplement DefaultParamHandler::updateMembers_()
94 
95 private:
96  double threshold_;
97 
98  // @}
99  };
100 
101 }
102 
103 #endif //OPENMS_FILTERING_TRANSFORMERS_THRESHOLDMOWER_H
Peak2D PeakType
Definition: MassTrace.h:48
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height)
Definition: Peak2D.h:167
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:50
double threshold_
Definition: ThresholdMower.h:96
void filterSpectrum(SpectrumType &spectrum)
Definition: ThresholdMower.h:74
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11