| OpenMS 2.5.0

ExtendedIsotopeModel.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
36 #pragma once
37
38 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
39
40 namespace OpenMS
41 {
55 class OPENMS_DLLAPI ExtendedIsotopeModel :
56 public InterpolationModel
57 {
58
59 public:
60 typedef InterpolationModel::CoordinateType CoordinateType;
61 typedef InterpolationModel::CoordinateType IntensityType;
62
63 enum Averagines {C = 0, H, N, O, S, AVERAGINE_NUM};
64
66 ExtendedIsotopeModel();
67
69 ExtendedIsotopeModel(const ExtendedIsotopeModel & source);
70
72 ~ExtendedIsotopeModel() override;
73
75 virtual ExtendedIsotopeModel & operator=(const ExtendedIsotopeModel & source);
76
77 UInt getCharge();
78
80 static BaseModel<1> * create()
81 {
82 return new ExtendedIsotopeModel();
83 }
84
86 static const String getProductName()
87 {
88 return "ExtendedIsotopeModel";
89 }
90
98 void setOffset(CoordinateType offset) override;
99
100 CoordinateType getOffset();
101
103 void setSamples() override;
104
107 CoordinateType getCenter() const override;
108
109 protected:
110 CoordinateType isotope_stdev_;
111 UInt charge_;
112 CoordinateType monoisotopic_mz_;
113 double averagine_[AVERAGINE_NUM];
114 Int max_isotope_;
115 double trim_right_cutoff_;
116 double isotope_distance_;
117
118 void updateMembers_() override;
119 };
120 }
121
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ExtendedIsotopeModel::isotope_stdev_
CoordinateType isotope_stdev_
Definition: ExtendedIsotopeModel.h:110
OpenMS::ExtendedIsotopeModel
Extended isotope distribution approximated using linear interpolation.
Definition: ExtendedIsotopeModel.h:55
OpenMS::ExtendedIsotopeModel::create
static BaseModel< 1 > * create()
create new ExtendedIsotopeModel object (needed by Factory)
Definition: ExtendedIsotopeModel.h:80
OpenMS::ExtendedIsotopeModel::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: ExtendedIsotopeModel.h:86
OpenMS::InterpolationModel
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:54
OpenMS::ExtendedIsotopeModel::Averagines
Averagines
Definition: ExtendedIsotopeModel.h:63
OpenMS::BaseModel< 1 >
OpenMS::ExtendedIsotopeModel::charge_
UInt charge_
Definition: ExtendedIsotopeModel.h:111
OpenMS::ExtendedIsotopeModel::max_isotope_
Int max_isotope_
Definition: ExtendedIsotopeModel.h:114
OpenMS::ExtendedIsotopeModel::IntensityType
InterpolationModel::CoordinateType IntensityType
Definition: ExtendedIsotopeModel.h:61
OpenMS::ExtendedIsotopeModel::CoordinateType
InterpolationModel::CoordinateType CoordinateType
Definition: ExtendedIsotopeModel.h:60
InterpolationModel.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ExtendedIsotopeModel::trim_right_cutoff_
double trim_right_cutoff_
Definition: ExtendedIsotopeModel.h:115
OpenMS::ExtendedIsotopeModel::S
Definition: ExtendedIsotopeModel.h:63
OpenMS::ExtendedIsotopeModel::isotope_distance_
double isotope_distance_
Definition: ExtendedIsotopeModel.h:116
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
double
int
OpenMS::ExtendedIsotopeModel::monoisotopic_mz_
CoordinateType monoisotopic_mz_
Definition: ExtendedIsotopeModel.h:112