OpenMS  2.8.0
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 2002-2021.
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;
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) const;
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
140 
141  // signal-to-noise window length
143 
144  // maximal spacing difference defining a missing data point
146 
147  // maximal spacing difference defining a large gap
149 
150  // maximum number of missing points
151  unsigned missing_;
152 
153  }; // end PeakPickerMaxima
154 
155 } // namespace OpenMS
156 
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerMaxima.h:67
double int_max
intensity value of the peak apex
Definition: PeakPickerMaxima.h:97
PeakPickerMaxima(double signal_to_noise, double spacing_difference=1.5, double spacing_difference_gap=4.0, double sn_window_length=200, unsigned missing=2)
Constructor.
int pos
index of the peak apex (relative to the input data)
Definition: PeakPickerMaxima.h:89
unsigned missing_
Definition: PeakPickerMaxima.h:151
double spacing_difference_
Definition: PeakPickerMaxima.h:145
double signal_to_noise_
Definition: PeakPickerMaxima.h:139
double spacing_difference_gap_
Definition: PeakPickerMaxima.h:148
double sn_window_length_
Definition: PeakPickerMaxima.h:142
double mz_max
m/z value of the peak apex
Definition: PeakPickerMaxima.h:95
int right_boundary
index of the right boundary (relative to the input data)
Definition: PeakPickerMaxima.h:93
void findMaxima(const std::vector< double > &mz_array, const std::vector< double > &int_array, std::vector< PeakCandidate > &pc, bool check_spacings=true) const
Will find local maxima in raw data.
void pick(std::vector< double > &mz_array, std::vector< double > &int_array, std::vector< PeakCandidate > &pc, bool check_spacings=true)
Will pick peaks in a spectrum.
virtual ~PeakPickerMaxima()
Destructor.
Definition: PeakPickerMaxima.h:76
int left_boundary
index of the left boundary (relative to the input data)
Definition: PeakPickerMaxima.h:91
The PeakCandidate describes the output of the peak picker.
Definition: PeakPickerMaxima.h:87
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47