OpenMS
Scaler.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 2002-2023.
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 
41 
42 #include <map>
43 
44 namespace OpenMS
45 {
51  class OPENMS_DLLAPI Scaler :
52  public DefaultParamHandler
53  {
54 public:
55 
56  // @name Constructors and Destructors
57  // @{
59  Scaler();
61  ~Scaler() override;
62 
64  Scaler(const Scaler & source);
66  Scaler & operator=(const Scaler & source);
67 
68  // @}
69 
70  // @name Accessors
71  // @{
72 
73  template <typename SpectrumType>
74  void filterSpectrum(SpectrumType & spectrum)
75  {
76  if (spectrum.empty()) return;
77 
78  spectrum.sortByIntensity();
79  typename SpectrumType::size_type count = spectrum.size();
80  ++count;
81  typename SpectrumType::PeakType::IntensityType last_int = 0.0;
82  typename SpectrumType::Iterator it = spectrum.end();
83  do
84  {
85  --it;
86  if (it->getIntensity() != last_int)
87  {
88  --count;
89  }
90  last_int = it->getIntensity();
91  it->setIntensity(count);
92  }
93  while (it != spectrum.begin());
94  }
95 
96  void filterPeakSpectrum(PeakSpectrum & spectrum);
97 
98  void filterPeakMap(PeakMap & exp);
99 
100  //TODO reimplement DefaultParamHandler::updateMembers_() when introducing member variables
101 
102  // @}
103 
104  };
105 
106 }
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:134
void sortByIntensity(bool reverse=false)
Lexicographically sorts the peaks by their intensity.
float IntensityType
Intensity type.
Definition: Peak1D.h:62
Scaler scales the peak by ranking the peaks and assigning intensity according to rank.
Definition: Scaler.h:53
void filterPeakSpectrum(PeakSpectrum &spectrum)
void filterPeakMap(PeakMap &exp)
Scaler()
default constructor
~Scaler() override
destructor
Scaler & operator=(const Scaler &source)
assignment operator
void filterSpectrum(SpectrumType &spectrum)
Definition: Scaler.h:74
Scaler(const Scaler &source)
copy constructor
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48