| OpenMS 2.5.0

EGHModel.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: Stephan Aiche $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
38 #include <OpenMS/MATH/STATISTICS/BasicStatistics.h>
39
40 #include <boost/math/tr1.hpp>
41
42 namespace OpenMS
43 {
55 class OPENMS_DLLAPI EGHModel :
56 public InterpolationModel
57 {
58
59 public:
60 typedef InterpolationModel::CoordinateType CoordinateType;
61 typedef Math::BasicStatistics<CoordinateType> BasicStatistics;
62 typedef LinearInterpolation::container_type ContainerType;
63
65 EGHModel();
66
68 EGHModel(const EGHModel & source);
69
71 ~EGHModel() override;
72
74 virtual EGHModel & operator=(const EGHModel & source);
75
77 static BaseModel<1> * create()
78 {
79 return new EGHModel();
80 }
81
83 static const String getProductName()
84 {
85 return "EGHModel";
86 }
87
89 void setOffset(CoordinateType offset) override;
90
92 void setSamples() override;
93
95 CoordinateType getCenter() const override;
96
97 protected:
98 CoordinateType min_;
99 CoordinateType max_;
100 BasicStatistics statistics_;
101 CoordinateType height_; // H in paper
102 CoordinateType apex_rt_;
103
104 CoordinateType A_;
105 CoordinateType B_;
106
107 CoordinateType tau_;
108 CoordinateType sigma_square_;
109 CoordinateType sigma_square_2_;
110
111
112 void updateMembers_() override;
113
115 void computeBoundaries_();
116
123 inline void evaluateEGH_(CoordinateType & rt, CoordinateType & egh_value)
124 {
125 CoordinateType denominator = sigma_square_2_ + tau_ * rt;
126
127 if (denominator > 0)
128 {
129 // evaluate egh ->
130 egh_value = height_ * exp(
131 (-1 * rt * rt) / denominator
132 );
133 }
134 else
135 {
136 egh_value = 0.0;
137 }
138 }
139
140 };
141
142 } // namespace OpenMS
143
OpenMS::EGHModel::B_
CoordinateType B_
Definition: EGHModel.h:105
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::EGHModel::apex_rt_
CoordinateType apex_rt_
Definition: EGHModel.h:102
OpenMS::EGHModel::sigma_square_2_
CoordinateType sigma_square_2_
Definition: EGHModel.h:109
OpenMS::EGHModel::BasicStatistics
Math::BasicStatistics< CoordinateType > BasicStatistics
Definition: EGHModel.h:61
OpenMS::Math::BasicStatistics< CoordinateType >
OpenMS::InterpolationModel
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:54
OpenMS::EGHModel::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: EGHModel.h:83
OpenMS::EGHModel::evaluateEGH_
void evaluateEGH_(CoordinateType &rt, CoordinateType &egh_value)
Evaluate the EGH function at position rt.
Definition: EGHModel.h:123
BasicStatistics.h
OpenMS::BaseModel< 1 >
OpenMS::EGHModel
Exponential-Gaussian hybrid distribution model for elution profiles.
Definition: EGHModel.h:55
OpenMS::EGHModel::height_
CoordinateType height_
Definition: EGHModel.h:101
OpenMS::EGHModel::min_
CoordinateType min_
Definition: EGHModel.h:98
InterpolationModel.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::EGHModel::ContainerType
LinearInterpolation::container_type ContainerType
Definition: EGHModel.h:62
OpenMS::EGHModel::sigma_square_
CoordinateType sigma_square_
Definition: EGHModel.h:108
OpenMS::EGHModel::create
static BaseModel< 1 > * create()
create new ElutionModel object (needed by Factory)
Definition: EGHModel.h:77
OpenMS::EGHModel::CoordinateType
InterpolationModel::CoordinateType CoordinateType
Definition: EGHModel.h:60
OpenMS::Math::LinearInterpolation< double >::container_type
std::vector< value_type > container_type
Definition: LinearInterpolation.h:84
double
OpenMS::EGHModel::max_
CoordinateType max_
Definition: EGHModel.h:99
OpenMS::EGHModel::A_
CoordinateType A_
Definition: EGHModel.h:104
OpenMS::EGHModel::statistics_
BasicStatistics statistics_
Definition: EGHModel.h:100
OpenMS::EGHModel::tau_
CoordinateType tau_
Definition: EGHModel.h:107