| OpenMS 2.5.0

PeakPickerMaxima.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: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/config.h>
38 #include <vector>
39
40 namespace OpenMS
41 {
42
66 class OPENMS_DLLAPI PeakPickerMaxima
67 {
68 public:
69
71 PeakPickerMaxima(double signal_to_noise, double spacing_difference = 1.5,
72 double spacing_difference_gap = 4.0, double sn_window_length = 200,
73 unsigned missing = 2);
74
76 virtual ~PeakPickerMaxima() {}
77
86 struct OPENMS_DLLAPI PeakCandidate
87 {
89 int pos;
91 int left_boundary;
93 int right_boundary;
95 double mz_max;
97 double int_max;
98 };
99
114 void findMaxima(const std::vector<double>& mz_array,
115 const std::vector<double>& int_array,
116 std::vector<PeakCandidate>& pc,
117 bool check_spacings = true);
118
131 void pick(std::vector<double>& mz_array,
132 std::vector<double>& int_array,
133 std::vector<PeakCandidate>& pc,
134 bool check_spacings = true);
135
136 protected:
137
138 // signal-to-noise parameter
139 double signal_to_noise_;
140
141 // signal-to-noise window length
142 double sn_window_length_;
143
144 // maximal spacing difference defining a missing data point
145 double spacing_difference_;
146
147 // maximal spacing difference defining a large gap
148 double spacing_difference_gap_;
149
150 // maximum number of missing points
151 unsigned missing_;
152
153 }; // end PeakPickerMaxima
154
155 } // namespace OpenMS
156
OpenMS::PeakPickerMaxima::sn_window_length_
double sn_window_length_
Definition: PeakPickerMaxima.h:142
OpenMS::PeakPickerMaxima::PeakCandidate::right_boundary
int right_boundary
index of the right boundary (relative to the input data)
Definition: PeakPickerMaxima.h:93
OpenMS::PeakPickerMaxima::PeakCandidate::pos
int pos
index of the peak apex (relative to the input data)
Definition: PeakPickerMaxima.h:89
OpenMS::PeakPickerMaxima::missing_
unsigned missing_
Definition: PeakPickerMaxima.h:151
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeakPickerMaxima::spacing_difference_
double spacing_difference_
Definition: PeakPickerMaxima.h:145
OpenMS::PeakPickerMaxima::PeakCandidate::mz_max
double mz_max
m/z value of the peak apex
Definition: PeakPickerMaxima.h:95
OpenMS::PeakPickerMaxima::PeakCandidate::int_max
double int_max
intensity value of the peak apex
Definition: PeakPickerMaxima.h:97
OpenMS::PeakPickerMaxima::spacing_difference_gap_
double spacing_difference_gap_
Definition: PeakPickerMaxima.h:148
OpenMS::PeakPickerMaxima::~PeakPickerMaxima
virtual ~PeakPickerMaxima()
Destructor.
Definition: PeakPickerMaxima.h:76
OpenMS::PeakPickerMaxima::signal_to_noise_
double signal_to_noise_
Definition: PeakPickerMaxima.h:139
OpenMS::PeakPickerMaxima::PeakCandidate
The PeakCandidate describes the output of the peak picker.
Definition: PeakPickerMaxima.h:86
OpenMS::PeakPickerMaxima
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerMaxima.h:66
OpenMS::PeakPickerMaxima::PeakCandidate::left_boundary
int left_boundary
index of the left boundary (relative to the input data)
Definition: PeakPickerMaxima.h:91