| OpenMS 2.5.0

PeakShape.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: Eva Lange $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <cmath>
39
40 #include <OpenMS/CONCEPT/Types.h>
41 #include <OpenMS/KERNEL/MSSpectrum.h>
42
43 namespace OpenMS
44 {
50 class OPENMS_DLLAPI PeakShape
51 {
52 public:
68 enum Type
69 {
70 LORENTZ_PEAK,
71 SECH_PEAK,
72 UNDEFINED
73 };
74
76 typedef MSSpectrum::const_iterator PeakIterator;
77
79 PeakShape();
80
82 PeakShape(double height_, double mz_position_, double left_width_, double right_width_, double area_, PeakIterator left_, PeakIterator right_, Type type_);
83
85 PeakShape(double height_, double mz_position_, double left_width_, double right_width_, double area_, Type type_);
86
87
89 PeakShape(const PeakShape & rhs);
90
92 virtual ~PeakShape();
93
95 PeakShape & operator=(const PeakShape & rhs);
96
97 //Equality operator
98 bool operator==(const PeakShape & rhs) const;
99 //Equality operator
100 bool operator!=(const PeakShape & rhs) const;
101
103 double operator()(double x) const;
105 double getSymmetricMeasure() const;
107 double getFWHM() const;
109 bool iteratorsSet() const;
110
111 PeakIterator getLeftEndpoint() const;
112 void setLeftEndpoint(PeakIterator left_endpoint);
113
114 PeakIterator getRightEndpoint() const;
115 void setRightEndpoint(PeakIterator right_endpoint);
117 double height;
119 double mz_position;
121 double left_width;
123 double right_width;
125 double area;
130 double r_value;
132 double signal_to_noise;
133
135 Type type;
136
140 class OPENMS_DLLAPI PositionLess
141 {
142 public:
143 inline bool operator()(const PeakShape & a, const PeakShape & b)
144 {
145 return a.mz_position < b.mz_position;
146 }
147
148 };
149 protected:
151 PeakIterator left_endpoint_;
153 PeakIterator right_endpoint_;
155 MSSpectrum exp_;
157 bool left_iterator_set_;
159 bool right_iterator_set_;
160 };
161 } // namespace OpenMS
162
OpenMS::PeakShape::Type
Type
Peak shape type (asymmetric Lorentzian or asymmetric hyperbolic secans squared).
Definition: PeakShape.h:68
OpenMS::PeakShape::right_width
double right_width
Right width parameter.
Definition: PeakShape.h:123
OpenMS::PeakShape::left_iterator_set_
bool left_iterator_set_
flag if left endpoint iterator differs from default value
Definition: PeakShape.h:157
OpenMS::PeakShape::mz_position
double mz_position
Centroid position.
Definition: PeakShape.h:119
OpenMS::PeakShape::left_endpoint_
PeakIterator left_endpoint_
Left peak endpoint in the data.
Definition: PeakShape.h:151
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::PeakShape::SECH_PEAK
Definition: PeakShape.h:71
Types.h
OpenMS::PeakShape::PositionLess
Comparison of mz_positions.
Definition: PeakShape.h:140
OpenMS::PeakShape::signal_to_noise
double signal_to_noise
The signal to noise ratio at the mz_position.
Definition: PeakShape.h:132
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::PeakShape::r_value
double r_value
Correlation coefficient.
Definition: PeakShape.h:130
OpenMS::PeakShape
Internal representation of a peak shape (used by the PeakPickerCWT)
Definition: PeakShape.h:50
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSSpectrum.h
OpenMS::PeakShape::height
double height
Maximum intensity of the peak shape.
Definition: PeakShape.h:117
OpenMS::PeakShape::area
double area
Area of the peak shape.
Definition: PeakShape.h:125
OpenMS::PeakShape::right_endpoint_
PeakIterator right_endpoint_
Right peak endpoint in the data.
Definition: PeakShape.h:153
OpenMS::PeakShape::left_width
double left_width
Left width parameter.
Definition: PeakShape.h:121
OpenMS::PeakShape::type
Type type
peak shape type
Definition: PeakShape.h:135
OpenMS::PeakShape::PeakIterator
MSSpectrum::const_iterator PeakIterator
Iterator to the raw data vector.
Definition: PeakShape.h:76
OpenMS::PeakShape::LORENTZ_PEAK
Definition: PeakShape.h:70
OpenMS::PeakShape::PositionLess::operator()
bool operator()(const PeakShape &a, const PeakShape &b)
Definition: PeakShape.h:143
OpenMS::PeakShape::right_iterator_set_
bool right_iterator_set_
flag if left endpoint iterator differs from default value
Definition: PeakShape.h:159
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
OpenMS::PeakShape::exp_
MSSpectrum exp_
Needed for initialization of endpoint iterators.
Definition: PeakShape.h:155