| OpenMS 2.5.0

ComplementFilter.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: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36
37 #include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
38
39 #include <map>
40 #include <cmath>
41
42 namespace OpenMS
43 {
51 class OPENMS_DLLAPI ComplementFilter :
52 public FilterFunctor
53 {
54 public:
55
56 // @name Constructors and Destructors
58 ComplementFilter();
60
62 ComplementFilter(const ComplementFilter & source);
63
65 ~ComplementFilter() override;
67
68 // @name Operators
70 ComplementFilter & operator=(const ComplementFilter & source);
73
74 // @name Accessors
76 static FilterFunctor * create() { return new ComplementFilter(); }
77
79 template <typename SpectrumType>
80 double apply(SpectrumType & spectrum)
81 {
82 if (spectrum.size() < 2)
83 {
84 return 0;
85 }
86 double tolerance = (double)param_.getValue("tolerance");
87 double parentmass = 0.0;
88 if (!spectrum.getPrecursors().empty()) parentmass = spectrum.getPrecursors()[0].getMZ();
89 double result(0);
90
91 spectrum.sortByPosition();
92
94 Size j = spectrum.size() - 1;
95 for (Size i = 0; i < spectrum.size() && i <= j; /*++i*/)
96 {
97 double sum = spectrum[i].getPosition()[0] + spectrum[j].getPosition()[0];
98
99 if (std::fabs(sum - parentmass) < tolerance)
100 {
101 result += spectrum[i].getIntensity() + spectrum[j].getIntensity();
102 }
103
104 if (sum < parentmass)
105 {
106 ++i;
107 }
108 else
109 {
110 if (sum > parentmass)
111 {
112 --j;
113 }
114 }
115 }
116
117 return result;
118 }
119
121 static const String getProductName()
122 {
123 return "ComplementFilter";
124 }
125
127
128 };
129 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ComplementFilter::getProductName
static const String getProductName()
returns the name for registration at the factory
Definition: ComplementFilter.h:121
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::ComplementFilter
total intensity of peak pairs that could result from complementing fragments of charge state 1 ...
Definition: ComplementFilter.h:51
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::ComplementFilter::apply
double apply(SpectrumType &spectrum)
returns the total intensity of peak pairs which could result from complementing fragments ...
Definition: ComplementFilter.h:80
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FilterFunctor
A FilterFunctor extracts some spectrum characteristics for quality assessment.
Definition: FilterFunctor.h:44
OpenMS::ComplementFilter::create
static FilterFunctor * create()
Definition: ComplementFilter.h:76
double
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
FilterFunctor.h
OpenMS::Math::sum
static double sum(IteratorType begin, IteratorType end)
Calculates the sum of a range of values.
Definition: StatisticFunctions.h:120
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127