OpenMS  3.0.0
NLargest.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 2002-2022.
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 #pragma once
36 
40 
43 
44 namespace OpenMS
45 {
46 
54  class OPENMS_DLLAPI NLargest :
55  public DefaultParamHandler
56  {
57 public:
58 
59  // @name Constructors and Destructors
60  // @{
61 
63  NLargest();
65  NLargest(UInt n);
67  ~NLargest() override;
68 
70  NLargest(const NLargest & source);
72  NLargest & operator=(const NLargest & source);
73 
74  // @}
75 
77  template <typename SpectrumType>
78  void filterSpectrum(SpectrumType & spectrum)
79  {
80  if (spectrum.size() <= peakcount_) return;
81 
82  // sort by reverse intensity
83  spectrum.sortByIntensity(true);
84 
85  // keep the n largest peaks if more than n are present
86  std::vector<Size> indices;
87  for (Size i = 0; i != peakcount_; ++i)
88  {
89  indices.push_back(i);
90  }
91  spectrum.select(indices);
92  }
93 
94  void filterPeakSpectrum(PeakSpectrum & spectrum);
95 
96  void filterPeakMap(PeakMap & exp);
97 
98  //TODO reimplement DefaultParamHandler::updateMembers_()
99 
100  // @}
101 
102 protected:
103  void updateMembers_() override;
105 
107  void init_();
108 
109  };
110 
111 }
DefaultParamHandler.h
OpenMS::MSSpectrum::select
MSSpectrum & select(const std::vector< Size > &indices)
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::NLargest
NLargest removes all but the n largest peaks.
Definition: NLargest.h:54
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MSSpectrum::sortByIntensity
void sortByIntensity(bool reverse=false)
Lexicographically sorts the peaks by their intensity.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
MSExperiment.h
OpenMS::NLargest::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: NLargest.h:78
OpenMS::NLargest::peakcount_
UInt peakcount_
Definition: NLargest.h:104
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h
MSSpectrum.h