| OpenMS 2.5.0

NeutralLossMarker.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/PeakMarker.h>
38
39 #include <map>
40 #include <cmath>
41
42 namespace OpenMS
43 {
51 class OPENMS_DLLAPI NeutralLossMarker :
52 public PeakMarker
53 {
54 public:
55
56 // @name Constructors and Destructors
57 // @{
59 NeutralLossMarker();
60
62 NeutralLossMarker(const NeutralLossMarker & source);
63
65 ~NeutralLossMarker() override;
66 // @}
67
68 // @name Operators
69 // @{
71 NeutralLossMarker & operator=(const NeutralLossMarker & source);
72 // @}
73
74 // @name Accessors
75 // @{
77 static PeakMarker * create() { return new NeutralLossMarker(); }
78
80 template <typename SpectrumType>
81 void apply(std::map<double, bool> & marked, SpectrumType & spectrum)
82 {
83 // how often a peak needs to be marked to be returned
84 double marks = (double)param_.getValue("marks");
85 double tolerance = (double)param_.getValue("tolerance");
86 std::map<double, SignedSize> ions_w_neutrallosses;
87 spectrum.sortByPosition();
88 for (Size i = 0; i < spectrum.size(); ++i)
89 {
90 double mz = spectrum[i].getPosition()[0];
91 double intensity = spectrum[i].getIntensity();
92 SignedSize j = i - 1;
93 while (j >= 0)
94 {
95 double curmz = spectrum[j].getPosition()[0];
96 double curIntensity = spectrum[j].getIntensity();
97
98 // check for peak that's a water or ammonia away
99 if (std::fabs(mz - curmz - 17) < tolerance || std::fabs(mz - curmz - 18) < tolerance)
100 {
101 // neutral loss peak should be smaller
102 if (curIntensity < intensity)
103 {
104 ions_w_neutrallosses[mz]++;
105 // neutral loss peak not marked
106 //ions_w_neutrallosses[curmz]++;
107 }
108 }
109 else
110 {
111 if (mz - curmz > 18.3)
112 {
113 break;
114 }
115 }
116 --j;
117 }
118 }
119
120 for (std::map<double, SignedSize>::const_iterator cmit = ions_w_neutrallosses.begin(); cmit != ions_w_neutrallosses.end(); ++cmit)
121 {
122 if (cmit->second >= marks)
123 {
124 marked.insert(std::pair<double, bool>(cmit->first, true));
125 }
126 }
127 return;
128 }
129
131 static const String getProductName()
132 {
133 return "NeutralLossMarker";
134 }
135
136 // @}
137
138 };
139
140 }
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::PeakMarker
PeakMarker marks peaks that seem to fulfill some criterion.
Definition: PeakMarker.h:47
PeakMarker.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::NeutralLossMarker::getProductName
static const String getProductName()
Definition: NeutralLossMarker.h:131
OpenMS::NeutralLossMarker::create
static PeakMarker * create()
Definition: NeutralLossMarker.h:77
double
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::NeutralLossMarker
NeutralLossMarker marks peak pairs which could represent an ion an its neutral loss (water...
Definition: NeutralLossMarker.h:51
OpenMS::NeutralLossMarker::apply
void apply(std::map< double, bool > &marked, SpectrumType &spectrum)
Definition: NeutralLossMarker.h:81
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127