| OpenMS 2.5.0

IsotopeModel.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Clemens Groepl, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
39 #include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
40
41 namespace OpenMS
42 {
43 class EmpiricalFormula;
44
58 class OPENMS_DLLAPI IsotopeModel :
59 public InterpolationModel
60 {
61
62 public:
63 typedef InterpolationModel::CoordinateType CoordinateType;
64 typedef InterpolationModel::CoordinateType IntensityType;
65
66 enum Averagines {C = 0, H, N, O, S, AVERAGINE_NUM};
67
69 IsotopeModel();
70
72 IsotopeModel(const IsotopeModel & source);
73
75 ~IsotopeModel() override;
76
78 virtual IsotopeModel & operator=(const IsotopeModel & source);
79
80 UInt getCharge();
81
83 static BaseModel<1> * create()
84 {
85 return new IsotopeModel();
86 }
87
89 static const String getProductName()
90 {
91 return "IsotopeModel";
92 }
93
101 void setOffset(CoordinateType offset) override;
102
103 CoordinateType getOffset();
104
106 EmpiricalFormula getFormula();
107
109 virtual void setSamples(const EmpiricalFormula & formula);
110
112 using InterpolationModel::setSamples;
113
118 CoordinateType getCenter() const override;
119
125 const IsotopeDistribution & getIsotopeDistribution() const;
126
127
128 protected:
129 CoordinateType isotope_stdev_;
130 CoordinateType isotope_lorentz_fwhm_;
131
132 UInt charge_;
133 CoordinateType mean_;
134 CoordinateType monoisotopic_mz_;
135 double averagine_[AVERAGINE_NUM];
136 Int max_isotope_;
137 double trim_right_cutoff_;
138 double isotope_distance_;
139 IsotopeDistribution isotope_distribution_;
140
141 void updateMembers_() override;
142
143 };
144 }
145
OpenMS::IsotopeModel::trim_right_cutoff_
double trim_right_cutoff_
Definition: IsotopeModel.h:137
OpenMS::IsotopeModel::S
Definition: IsotopeModel.h:66
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IsotopeModel::monoisotopic_mz_
CoordinateType monoisotopic_mz_
Definition: IsotopeModel.h:134
OpenMS::IsotopeModel::isotope_lorentz_fwhm_
CoordinateType isotope_lorentz_fwhm_
Definition: IsotopeModel.h:130
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::InterpolationModel
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:54
OpenMS::BaseModel< 1 >
OpenMS::IsotopeModel::isotope_distribution_
IsotopeDistribution isotope_distribution_
Definition: IsotopeModel.h:139
OpenMS::IsotopeModel
Isotope distribution approximated using linear interpolation.
Definition: IsotopeModel.h:58
IsotopeDistribution.h
OpenMS::IsotopeModel::charge_
UInt charge_
Definition: IsotopeModel.h:132
OpenMS::IsotopeModel::mean_
CoordinateType mean_
Definition: IsotopeModel.h:133
OpenMS::IsotopeModel::IntensityType
InterpolationModel::CoordinateType IntensityType
Definition: IsotopeModel.h:64
InterpolationModel.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::IsotopeModel::Averagines
Averagines
Definition: IsotopeModel.h:66
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IsotopeModel::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: IsotopeModel.h:89
double
OpenMS::InterpolationModel::setSamples
virtual void setSamples()
set sample/supporting points of interpolation wrt params.
Definition: InterpolationModel.h:161
OpenMS::IsotopeModel::isotope_distance_
double isotope_distance_
Definition: IsotopeModel.h:138
int
OpenMS::IsotopeModel::CoordinateType
InterpolationModel::CoordinateType CoordinateType
Definition: IsotopeModel.h:63
OpenMS::IsotopeModel::create
static BaseModel< 1 > * create()
create new IsotopeModel object (needed by Factory)
Definition: IsotopeModel.h:83
OpenMS::IsotopeModel::isotope_stdev_
CoordinateType isotope_stdev_
Definition: IsotopeModel.h:129
OpenMS::IsotopeModel::max_isotope_
Int max_isotope_
Definition: IsotopeModel.h:136