| OpenMS 2.5.0

SqrtMower.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 2002-2020.
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
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/KERNEL/MSSpectrum.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 #include <cmath>
43
44 namespace OpenMS
45 {
51 class OPENMS_DLLAPI SqrtMower :
52 public DefaultParamHandler
53 {
54 public:
55
56 // @name Constructors and Destructors
57 // @{
59 SqrtMower();
61 ~SqrtMower() override;
62
64 SqrtMower(const SqrtMower & source);
66 SqrtMower & operator=(const SqrtMower & source);
67 // @}
68
70 template <typename SpectrumType>
71 void filterSpectrum(SpectrumType & spectrum)
72 {
73 bool warning = false;
74 for (typename SpectrumType::Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
75 {
76 double intens = it->getIntensity();
77 if (intens < 0)
78 {
79 intens = 0;
80 warning = true;
81 }
82 it->setIntensity(std::sqrt(intens));
83 }
84 if (warning)
85 {
86 std::cerr << "Warning negative intensities were set to zero" << std::endl;
87 }
88 return;
89 }
90
91 void filterPeakSpectrum(PeakSpectrum & spectrum);
92
93 void filterPeakMap(PeakMap & exp);
94
95 //TODO reimplement DefaultParamHandler::updateMembers_()
96
97 // @}
98
99 };
100
101 }
102
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MSSpectrum::Iterator
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:102
StandardTypes.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::SqrtMower
Scales the intensity of peaks to the sqrt.
Definition: SqrtMower.h:51
OpenMS::SqrtMower::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: SqrtMower.h:71
DefaultParamHandler.h
MSSpectrum.h